41 research outputs found
Car-Parrinello molecular dynamics simulations of Na⁺–Cl⁻ ion pair in liquid water
The aqueous solvation shell of a Na⁺–Cl⁻ pair is studied using Car-Parrinello
molecular dynamics simulations. Water-mediated and contact states
of the ion pair are investigated. The first hydration shell of the Na⁺ ion
is found to be octahedral with one vacant position for both states. In the
contact state one of the water molecules is substituted by the Cl⁻ ion.
The first hydration shell of the Cl⁻ is less structured and strongly effected
by the proximity of the Na⁺ in the contact state. The oxygen coordination
numbers for Na⁺ and Cl⁻ are 4.9 and 5.6 for the water-mediated state, and
3.6 and 6.4 for the contact state. The corresponding hydrogen coordination
numbers are 10.9 and 5.2; 9.2 and 3.9, respectively.Методами молекулярної динаміки Кара-Паррінелло вивчалася гідратна оболонка іонної пари Na⁺–Cl⁻. Досліджувалися медійований водою та контактний стан іонної пари. Знайдено, що перша гідратна оболонка іону Na⁺ є виражено октаедричною в обох станах. У контактному стані має місце заміщення однієї з молекул води іоном хлору. Перша гідратна оболонка іону Cl⁻ є менш структурованою й на неї сильніше впливає близькість іону натрію у контактній парі. Кисневі координаційні числа іонів натрію і хлору дорівнюють 4.9 та 5.6 для медійованого водою стану, та 3.6 і 6.4 для контактного стану іонної пари. Відповідні водневі координаційні числа становлять 10.9 і 5.2 та 9.2 і 3.9
Attractive Interactions Between Rod-like Polyelectrolytes: Polarization, Crystallization, and Packing
We study the attractive interactions between rod-like charged polymers in
solution that appear in the presence of multi-valence counterions. The
counterions condensed to the rods exhibit both a strong transversal
polarization and a longitudinal crystalline arrangement. At short distances
between the rods, the fraction of condensed counterions increases, and the
majority of these occupy the region between the rods, where they minimize their
repulsive interactions by arranging themselves into packing structures. The
attractive interaction is strongest for multivalent counterions. Our model
takes into account the hard-core volume of the condensed counterions and their
angular distribution around the rods. The hard core constraint strongly
suppresses longitudinal charge fluctuations.Comment: 4 figures, uses revtex, psfig and epsf. The new version contains a
different introduction, and the bibliography has been expande
Lattice-switch Monte Carlo
We present a Monte Carlo method for the direct evaluation of the difference
between the free energies of two crystal structures. The method is built on a
lattice-switch transformation that maps a configuration of one structure onto a
candidate configuration of the other by `switching' one set of lattice vectors
for the other, while keeping the displacements with respect to the lattice
sites constant. The sampling of the displacement configurations is biased,
multicanonically, to favor paths leading to `gateway' arrangements for which
the Monte Carlo switch to the candidate configuration will be accepted. The
configurations of both structures can then be efficiently sampled in a single
process, and the difference between their free energies evaluated from their
measured probabilities. We explore and exploit the method in the context of
extensive studies of systems of hard spheres. We show that the efficiency of
the method is controlled by the extent to which the switch conserves correlated
microstructure. We also show how, microscopically, the procedure works: the
system finds gateway arrangements which fulfill the sampling bias
intelligently. We establish, with high precision, the differences between the
free energies of the two close packed structures (fcc and hcp) in both the
constant density and the constant pressure ensembles.Comment: 34 pages, 9 figures, RevTeX. To appear in Phys. Rev.
Adsorption of mono- and multivalent cat- and anions on DNA molecules
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose
nucleic acid (DNA) molecule from a salt solution is investigated by computer
simulation. The ions are modelled as charged hard spheres, the DNA molecule as
a point charge pattern following the double-helical phosphate strands. The
geometrical shape of the DNA molecules is modelled on different levels ranging
from a simple cylindrical shape to structured models which include the major
and minor grooves between the phosphate strands. The densities of the ions
adsorbed on the phosphate strands, in the major and in the minor grooves are
calculated. First, we find that the adsorption pattern on the DNA surface
depends strongly on its geometrical shape: counterions adsorb preferentially
along the phosphate strands for a cylindrical model shape, but in the minor
groove for a geometrically structured model. Second, we find that an addition
of monovalent salt ions results in an increase of the charge density in the
minor groove while the total charge density of ions adsorbed in the major
groove stays unchanged. The adsorbed ion densities are highly structured along
the minor groove while they are almost smeared along the major groove.
Furthermore, for a fixed amount of added salt, the major groove cationic charge
is independent on the counterion valency. For increasing salt concentration the
major groove is neutralized while the total charge adsorbed in the minor groove
is constant. DNA overcharging is detected for multivalent salt. Simulations for
a larger ion radii, which mimic the effect of the ion hydration, indicate an
increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure
Effective interaction between helical bio-molecules
The effective interaction between two parallel strands of helical
bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using
computer simulations of the "primitive" model of electrolytes. In particular we
study a simple model for B-DNA incorporating explicitly its charge pattern as a
double-helix structure. The effective force and the effective torque exerted
onto the molecules depend on the central distance and on the relative
orientation. The contributions of nonlinear screening by monovalent counterions
to these forces and torques are analyzed and calculated for different salt
concentrations. As a result, we find that the sign of the force depends
sensitively on the relative orientation. For intermolecular distances smaller
than it can be both attractive and repulsive. Furthermore we report a
nonmonotonic behaviour of the effective force for increasing salt
concentration. Both features cannot be described within linear screening
theories. For large distances, on the other hand, the results agree with linear
screening theories provided the charge of the bio-molecules is suitably
renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog
Reexamination of the long-range Potts model: a multicanonical approach
We investigate the critical behavior of the one-dimensional q-state Potts
model with long-range (LR) interaction , using a multicanonical
algorithm. The recursion scheme initially proposed by Berg is improved so as to
make it suitable for a large class of LR models with unequally spaced energy
levels. The choice of an efficient predictor and a reliable convergence
criterion is discussed. We obtain transition temperatures in the first-order
regime which are in far better agreement with mean-field predictions than in
previous Monte Carlo studies. By relying on the location of spinodal points and
resorting to scaling arguments, we determine the threshold value
separating the first- and second-order regimes to two-digit precision within
the range . We offer convincing numerical evidence supporting
$\sigma_c(q)Comment: 18 pages, 18 figure
Computational Physics on Graphics Processing Units
The use of graphics processing units for scientific computations is an
emerging strategy that can significantly speed up various different algorithms.
In this review, we discuss advances made in the field of computational physics,
focusing on classical molecular dynamics, and on quantum simulations for
electronic structure calculations using the density functional theory, wave
function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012,
Helsinki, Finland, June 10-13, 201
Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions
The osmotic virial coefficient of globular protein solutions is
calculated as a function of added salt concentration at fixed pH by computer
simulations of the ``primitive model''. The salt and counter-ions as well as a
discrete charge pattern on the protein surface are explicitly incorporated. For
parameters roughly corresponding to lysozyme, we find that first
decreases with added salt concentration up to a threshold concentration, then
increases to a maximum, and then decreases again upon further raising the ionic
strength. Our studies demonstrate that the existence of a discrete charge
pattern on the protein surface profoundly influences the effective interactions
and that non-linear Poisson Boltzmann and Derjaguin-Landau-Verwey-Overbeek
(DLVO) theory fail for large ionic strength. The observed non-monotonicity of
is compared to experiments. Implications for protein crystallization are
discussed.Comment: 43 pages, including 17 figure